tbuckley/cabot-search huggingface dataset:
Plasma metabolomics study in screening and differential diagnosis of multiple primary lung cancer
Authors: Zixu Liu, Ling Wang, Shugeng Gao, Qi Xue, Fengwei Tan, Zhili Li, Yushun Gao
Journal: International Journal of Surgery (2023)

Multiple primary lung cancer (MPLC) is becoming increasingly common in clinical practice. Imaging examination is sometimes difficult to differentiate from intrapulmonary metastasis (IM) or single primary lung cancer (SPLC) before surgery. There is a lack of effective blood biomarkers as an auxiliary diagnostic method.A total of 179 patients who were hospitalized and operated in our department from January to June 2019 were collected, and they were divided into SPLC with 136 patients, MPLC with 24 patients, and IM with 19 patients. In total, 96 healthy people without lung cancer were enrolled. Medical history, imaging, and pathology data were assembled from all participants. Plasma metabolomics analysis was performed by quadrupole time-of-flight tandem mass spectrometry, and data were analyzed using SPSS19.0/Simca 14.1/MetaboAnalyst5.0 software. Significant metabolites were selected by variable importance in projection, P value, and fold change. The area under the receiver operating characteristic curve was used to evaluate their diagnostic ability.There were significant differences in plasma metabolite profiles between IM and MPLC. Seven metabolites were screened out. Two metabolites had higher levels in IM, and five metabolites had higher levels in MPLC. All had favorable discriminating capacity. Phosphatidyl ethanolamine (38:5) showed the highest sensitivity (0.95) and specificity (0.92). It was followed by l -histidine with sensitivity 0.92 and specificity 0.84. l -tyrosine can be used to identify SPLC and MPLC. The panel composed of related metabolites exhibited higher diagnostic ability. Eight principal metabolites caused remarkable differences between healthy people and MPLC, and five of them had area under the curves greater than 0.85, showing good discriminating power.Through the study of plasma metabolomics, it was found that there were obvious differences in the metabolite profiles of MPLC, IM, SPLC, and the healthy population. Some discovered metabolites possessed excellent diagnostic competence with high sensitivity and specificity. They had the potential to act as biomarkers for the screening and differential diagnosis of MPLCs.
Oncologic outcomes of intersphincteric resection versus abdominoperineal resection for lower rectal cancer: a systematic review and meta-analysis
Authors: Qiang Du, Wenming Yang, Jianhao Zhang, Siyuan Qiu, Xueting Liu, Yong Wang, Lie Yang, Zongguang Zhou
Journal: International Journal of Surgery (2023)

The efficacy of intersphincteric resection (ISR) surgery for patients with lower rectal cancer remains unclear compared to abdominoperineal resection (APR). The aim of this study is to compare the oncologic outcomes for lower rectal cancer patients after ISR and APR through a systematic review and meta-analysis.
Protection against the recent Monkeypox outbreaks: what options do we have? Correspondence
Authors: Ramadan Abdelmoez Farahat, Amira Y. Benmelouka, Emery Manirambona, Amro A. El-Sakka, Tareq Al-Ahdal, Khaled Albakri, Abdelaziz Abdelaal, Basel Abdelazeem, Ranjit Sah, Alfonso J. Rodriguez-Morales
Journal: International Journal of Surgery (2023)

Farahat, Ramadan Abdelmoez MBBCh; Benmelouka, Amira Y.; Manirambona, Emery MD; El-Sakka, Amro A. MD; Al-Ahdal, Tareq MSc; Albakri, Khaled; Abdelaal, Abdelaziz; Abdelazeem, Basel MD; Sah, Ranjit MD; Rodriguez-Morales, Alfonso J. MD, HonDSc Author Information
An easy-to-use artificial intelligence preoperative lymph node metastasis predictor (LN-MASTER) in rectal cancer based on a privacy-preserving computing platform: multicenter retrospective cohort study
Authors: Xu Guan, Guanyu Yu, Weiyuan Zhang, Rongbo Wen, Ran Wei, Shuai Jiao, Qing Zhao, Zheng Lou, Liqiang Hao, Enrui Liu, Xianhua Gao, Guiyu Wang, Wei Zhang, Xishan Wang
Journal: International Journal of Surgery (2023)

Background: Although the surgical treatment strategy for rectal cancer (RC) is usually based on the preoperative diagnosis of lymph node metastasis (LNM), the accurate diagnosis of LNM has been a clinical challenge. In this study, we developed machine learning (ML) models to predict the LNM status before surgery based on a privacy-preserving computing platform (PPCP) and created a web tool to help clinicians with treatment-based decision-making in RC patients. Patients and methods: A total of 6578 RC patients were enrolled in this study. ML models, including logistic regression, support vector machine, extreme gradient boosting (XGB), and random forest, were used to establish the prediction models. The areas under the receiver operating characteristic curves (AUCs) were calculated to compare the accuracy of the ML models with the US guidelines and clinical diagnosis of LNM. Last, model establishment and validation were performed in the PPCP without the exchange of raw data among different institutions. Results: LNM was detected in 1006 (35.3%), 252 (35.3%), 581 (32.9%), and 342 (27.4%) RC patients in the training, test, and external validation sets 1 and 2, respectively. The XGB model identified the optimal model with an AUC of 0.84 [95% confidence interval (CI), 0.83–0.86] compared with the logistic regression model (AUC, 0.76; 95% CI, 0.74–0.78), random forest model (AUC, 0.82; 95% CI, 0.81–0.84), and support vector machine model (AUC, 0.79; 95% CI, 0.78–0.81). Furthermore, the XGB model showed higher accuracy than the predictive factors of the US guidelines and clinical diagnosis. The predictive XGB model was embedded in a web tool (named LN-MASTER) to predict the LNM status for RC. Conclusion: The proposed easy-to-use model showed good performance for LNM prediction, and the web tool can help clinicians make treatment-based decisions for patients with RC. Furthermore, PPCP enables state-of-the-art model development despite the limited local data availability.
Postoperative mortality in Africa: are there any improvements in the last decade?
Authors: Wireko A. Awuah, Jyi Cheng Ng, Abubakar Nazir, Pearl O. Tenkorang, Rohan Yarlagadda, Jacob Kalmanovich, Toufik Abdul-Rahman, Aymar Akilimali, Vladyslav Sikora, Arda Isik
Journal: International Journal of Surgery (2023)

Awuah, Wireko A. MBBS; Ng, Jyi Cheng MD; Nazir, Abubakar MBBS; Tenkorang, Pearl O. MBChB; Yarlagadda, Rohan BS; Kalmanovich, Jacob BS, MD; Abdul-Rahman, Toufik MBBS; Akilimali, Aymar MD; Sikora, Vladyslav MD, PhD; Isik, Arda Facs, MD Author Information
Addressing Africa’s outrageous neurosurgeons deficit: what could the problem be?
Authors: Andrew A. Wireko, Pearl O. Tenkorang, Jyi Cheng Ng, Lian David, Rohan Yarlagadda, Toufik Abdul-Rahman, Vladyslav Sikora, Arda Isik
Journal: International Journal of Surgery (2023)

Wireko, Andrew A. MBBS; Tenkorang, Pearl O. MBChB; Ng, Jyi Cheng MD; David, Lian MBBS; Yarlagadda, Rohan BS; Abdul-Rahman, Toufik MBBS; Sikora, Vladyslav MD, PhD; Isik, Arda FEBS, FACS, MD Author Information
Plasma phospho-tau in Alzheimer’s disease: towards diagnostic and therapeutic trial applications
Authors: Fernando Gonzalez-Ortiz, Przemysław R. Kac, Wagner S. Brum, Henrik Zetterberg, Kaj Blennow, Thomas K. Karikari
Journal: Molecular Neurodegeneration (2023)

As the leading cause of dementia, Alzheimer's disease (AD) is a major burden on affected individuals, their families and caregivers, and healthcare systems. Although AD can be identified and diagnosed by cerebrospinal fluid or neuroimaging biomarkers that concord with neuropathological evidence and clinical symptoms, challenges regarding practicality and accessibility hinder their widespread availability and implementation. Consequently, many people with suspected cognitive impairment due to AD do not receive a biomarker-supported diagnosis. Blood biomarkers have the capacity to help expand access to AD diagnostics worldwide. One such promising biomarker is plasma phosphorylated tau (p-tau), which has demonstrated specificity to AD versus non-AD neurodegenerative diseases, and will be extremely important to inform on clinical diagnosis and eligibility for therapies that have recently been approved. This review provides an update on the diagnostic and prognostic performances of plasma p-tau181, p-tau217 and p-tau231, and their associations with in vivo and autopsy-verified diagnosis and pathological hallmarks. Additionally, we discuss potential applications and unanswered questions of plasma p-tau for therapeutic trials, given their recent addition to the biomarker toolbox for participant screening, recruitment and during-trial monitoring. Outstanding questions include assay standardization, threshold generation and biomarker verification in diverse cohorts reflective of the wider community attending memory clinics and included in clinical trials.
The rising cases of dengue amidst the prolonged monsoon in Pakistan: Challenges, efforts and recommendations
Authors: Hira Anas Khan, Umer Usman Malik, Juvairia Yousuf, Abeer Shahzad, Mati Ur Rehman, Zoaib Habib Tharwani
Journal: International Journal of Surgery (2023)

Khan, Hira Anas; Malik, Umer Usman; Yousuf, Juvairia; Shahzad, Abeer; Ur Rehman, Mati; Tharwani, Zoaib Habib Author Information
Secreted mammalian DNases protect against systemic bacterial infection by digesting biofilms
Authors: Keenan A. Lacey, Lee Serpas, Sohei Makita, Yueyang Wang, Ali Rashidfarrokhi, Chetna Soni, Sandra Gonzalez, Andre Moreira, Victor J. Torres, Boris Reizis
Journal: The Journal of Experimental Medicine (2023)

Extracellular DNase DNASE1L3 maintains tolerance to self-DNA in humans and mice, whereas the role of its homolog DNASE1 remains controversial, and the overall function of secreted DNases in immunity is unclear. We report that deletion of murine DNASE1 neither caused autoreactivity in isolation nor exacerbated lupus-like disease in DNASE1L3-deficient mice. However, combined deficiency of DNASE1 and DNASE1L3 rendered mice susceptible to bloodstream infection with Staphylococcus aureus. DNASE1/DNASE1L3 double-deficient mice mounted a normal innate response to S. aureus and did not accumulate neutrophil extracellular traps (NETs). However, their kidneys manifested severe pathology, increased bacterial burden, and biofilm-like bacterial lesions that contained bacterial DNA and excluded neutrophils. Furthermore, systemic administration of recombinant DNASE1 protein during S. aureus infection rescued the mortality of DNase-deficient mice and ameliorated the disease in wild-type mice. Thus, DNASE1 and DNASE1L3 jointly facilitate the control of bacterial infection by digesting extracellular microbial DNA in biofilms, suggesting the original evolutionary function of secreted DNases as antimicrobial agents.
Inhibition of ERK1/2 signaling prevents bone marrow fibrosis by reducing osteopontin plasma levels in a myelofibrosis mouse model
Authors: Elisa Bianchi, Sebastiano Rontauroli, Lara Tavernari, Margherita Mirabile, Francesca Pedrazzi, Elena Genovese, Stefano Sartini, Massimiliano Dall’Ora, Giulia Grisendi, Luca Fabbiani, Monica Maccaferri, Chiara Carretta, Sandra Parenti, Sebastian Fantini, Niccolò Bartalucci, Laura Calabresi, Manjola Balliu, Paola Guglielmelli, Leonardo Potenza, Enrico Tagliafico, Lorena Losi, Massimo Dominici, Mario Luppi, Alessandro Maria Vannucchi, Rossella Manfredini
Journal: Leukemia (2023)

Abstract Clonal myeloproliferation and development of bone marrow (BM) fibrosis are the major pathogenetic events in myelofibrosis (MF). The identification of novel antifibrotic strategies is of utmost importance since the effectiveness of current therapies in reverting BM fibrosis is debated. We previously demonstrated that osteopontin (OPN) has a profibrotic role in MF by promoting mesenchymal stromal cells proliferation and collagen production. Moreover, increased plasma OPN correlated with higher BM fibrosis grade and inferior overall survival in MF patients. To understand whether OPN is a druggable target in MF, we assessed putative inhibitors of OPN expression in vitro and identified ERK1/2 as a major regulator of OPN production. Increased OPN plasma levels were associated with BM fibrosis development in the Romiplostim-induced MF mouse model. Moreover, ERK1/2 inhibition led to a remarkable reduction of OPN production and BM fibrosis in Romiplostim-treated mice. Strikingly, the antifibrotic effect of ERK1/2 inhibition can be mainly ascribed to the reduced OPN production since it could be recapitulated through the administration of anti-OPN neutralizing antibody. Our results demonstrate that OPN is a novel druggable target in MF and pave the way to antifibrotic therapies based on the inhibition of ERK1/2-driven OPN production or the neutralization of OPN activity.
Research progress in spike mutations of SARS‐CoV‐2 variants and vaccine development
Authors: Xuemei He, Cai He, Weiqi Hong, Jingyun Yang, Xiawei Wei
Journal: Medicinal Research Reviews (2023)

Abstract The coronavirus disease 2019 (COVID‐19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID‐19 convalescent or vaccinated individuals is decreased against SARS‐CoV‐2 variants. Moreover, the vaccine effectiveness of current COVID‐19 vaccines against SARS‐CoV‐2 VOCs is not as high as that against wild‐type SARS‐CoV‐2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS‐CoV‐2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS‐CoV‐2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
A systematic review of associations between gut microbiota composition and growth failure in preterm neonates
Authors: Larissa L. Neves, Amy B. Hair, Geoffrey A. Preidis
Journal: Gut Microbes (2023)

Growth failure is among the most prevalent and devastating consequences of prematurity. Up to half of all extremely preterm neonates struggle to grow despite modern nutrition practices. Although elegant preclinical models suggest causal roles for the gut microbiome, these insights have not yet translated into biomarkers that identify at-risk neonates or therapies that prevent or treat growth failure. This systematic review aims to identify features of the neonatal gut microbiota that are positively or negatively associated with early postnatal growth. We identified 860 articles, of which 14 were eligible for inclusion. No two studies used the same definitions of growth, ages at stool collection, and statistical methods linking microbiota to metadata. In all, 58 different taxa were associated with growth, with little consensus among studies. Two or more studies reported positive associations with Enterobacteriaceae, Bacteroides, Bifidobacterium, Enterococcus, and Veillonella, and negative associations with Citrobacter, Klebsiella, and Staphylococcus. Streptococcus was positively associated with growth in five studies and negatively associated with growth in three studies. To gain insight into how the various definitions of growth could impact results, we performed an exploratory secondary analysis of 245 longitudinally sampled preterm infant stools, linking microbiota composition to multiple clinically relevant definitions of neonatal growth. Within this cohort, every definition of growth was associated with a different combination of microbiota features. Together, these results suggest that the lack of consensus in defining neonatal growth may limit our capacity to detect consistent, meaningful clinical associations that could be leveraged into improved care for preterm neonates.
The evolution of acute lymphoblastic leukemia research and therapy at MD Anderson over four decades
Authors: Elias Jabbour, Nicholas J. Short, Nitin Jain, Fadi G. Haddad, Mary Alma Welch, Farhad Ravandi, Hagop Kantarjian
Journal: Journal of Hematology & Oncology (2023)

Progress in the research and therapy of adult acute lymphoblastic leukemia (ALL) is accelerating. This analysis summarizes the data derived from the clinical trials conducted at MD Anderson between 1985 and 2022 across ALL subtypes. In Philadelphia chromosome-positive ALL, the addition of BCR::ABL1 tyrosine kinase inhibitors (TKIs) to intensive chemotherapy since 2000, improved outcomes. More recently, a chemotherapy-free regimen with blinatumomab and ponatinib resulted in a complete molecular remission rate of 85% and an estimated 3-year survival rate of 90%, potentially reducing the role of, and need for allogeneic stem cell transplantation (SCT) in remission. In younger patients with pre-B Philadelphia chromosome-negative ALL, the integration of blinatumomab and inotuzumab into the frontline therapy has improved the estimated 3-year survival rate to 85% across all risk categories. Our future strategy is to evaluate the early integration of both immunotherapy agents, inotuzumab and blinatumomab, with low-dose chemotherapy (dose-dense mini-Hyper-CVD-inotuzumab-blinatumomab) into the frontline setting followed by CAR T cells consolidation in high-risk patients, without any further maintenance therapy. In older patients, using less intensive chemotherapy (mini-Hyper-CVD) in combination with inotuzumab and blinatumomab has improved the 5-year survival rate to 50%. Among patients ≥ 65-70 years, the mortality in complete remission (CR) is still high and is multifactorial (old age, death in CR with infections, development of myelodysplastic syndrome or acute myeloid leukemia). A chemotherapy-free regimen with inotuzumab and blinatumomab is being investigated. The assessment of measurable residual disease (MRD) by next-generation sequencing (NGS) is superior to conventional assays, with early MRD negativity by NGS being associated with the best survival. We anticipate that the future therapy in B-ALL will involve less intensive and shorter chemotherapy regimens in combination with agents targeting CD19 (blinatumomab), CD20, and CD22 (inotuzumab). The optimal timing and use of CAR T cells therapy may be in the setting of minimal disease, and future trials will assess the role of CAR T cells as a consolidation among high-risk patients to replace allogeneic SCT. In summary, the management of ALL has witnessed significant progress during the past four decades. Novel combination regimens including newer-generation BCR::ABL1 TKIs and novel antibodies are questioning the need and duration of intensive chemotherapy and allogeneic SCT.
Correction: Development of a 4-aminopyrazolo[3,4-d]pyrimidine-based dual IGF1R/Src inhibitor as a novel anticancer agent with minimal toxicity
Authors: Ho Jin Lee, Phuong Chi Pham, Seung Yeob Hyun, Byungyeob Baek, Byungjin Kim, Yunha Kim, Hye-Young Min, Jeeyeon Lee, Ho-Young Lee
Journal: Molecular Cancer (2023)
Correction: Circular RNA circCORO1C promotes laryngeal squamous cell carcinoma progression by modulating the let-7c-5p/PBX3 axis
Authors: Yongyan Wu, Yuliang Zhang, Xiwang Zheng, Fengsheng Dai, Yan Lu, Li Dai, Min Niu, Huina Guo, Wenqi Li, Xuting Xue, Yunfeng Bo, Yujia Guo, Jiangbo Qin, Yixiao Qin, Hongliang Liu, Yu Zhang, Tao Yang, Li Li, Linshi Zhang, Rui Hou, Shuxin Wen, Changming An, Huizheng Li, Wei Xu, Wei Gao
Journal: Molecular Cancer (2023)

In our research published [1] in Molecular Cancer entitled "Circular RNA circCORO1C promotes laryngeal squamous cell carcinoma progression by modulating the let-7c-5p/PBX3 axis" (Molecular Cancer 19, Article number: 99 ( 2020)), we identified minor errors in the images presented in Figs.5E and 6L recently.Specifically, overlap was found in the representative migration images between the "TU-177 let-7c-5p inhibitor" group of Fig. 5E (row
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
Authors: Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T. Weirauch, Louis J. Muglia, Li Wang, Yaping Liu
Journal: Genome biology (2023)

Abstract Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single-nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.
Emergency Department Visits by Incarcerated Adults for Nonfatal Injuries — United States, 2010–2019
Authors: Avital Wulz, Gabrielle Miller, Livia Navon, Jill Daugherty
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

During 2010-2019, U.S. correctional authorities held 1.4-1.6 million persons in state and federal prisons annually, and 10.3-12.9 million persons were admitted to local jails each year (1,2). Incarcerated persons experience a disproportionate burden of negative health outcomes, including unintentional and violence-related injuries (3,4). No national studies on injury-related emergency department (ED) visits by incarcerated persons have been conducted, but a previous study demonstrated a high rate of such visits among a Seattle, Washington jail population (5). To examine nonfatal injury-related ED visits among incarcerated adults, CDC analyzed 2010-2019 National Electronic Injury Surveillance System-All Injury Program (NEISS-AIP) data. During 2010-2019, an estimated 733,547 ED visits by incarcerated adults occurred in the United States. The proportion of ED visits resulting from assault* and self-harm among incarcerated adults was five times as high as those among nonincarcerated adults. Among incarcerated adults, men and adult persons aged <65 years had the highest proportion of assault-related ED visits. Falls accounted for the most ED visits among incarcerated adults aged ≥65 years. A higher proportion of ED visits by incarcerated women than incarcerated men were for overdose or poisoning. These findings suggest that injuries among incarcerated adults differ from those among nonincarcerated adults and might require development and implementation of age- and sex-specific prevention strategies for this population.
<i>QuickStats:</i> Age-Adjusted Drug Overdose Death Rates,*<sup>,</sup>† by State — National Vital Statistics System, United States, 2021
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

DC 63.6-90.9 48.1-63.5 32.4-48.0 22.3-32.3 11.4-22.2 * Deaths per 100,000 standard population.Age-adjusted drug overdose death rates were calculated using the direct method and the 2000 U.S. Census Bureau standard population.In 2021, the age-adjusted drug overdose death rate was 32.4 per 100,000 standard population.† Drug overdose deaths were identified using International Classification of Diseases, Tenth Revision underlying cause-of-death codes X40-X44, X60-X64, X85, and Y10-Y14.In 2021, the U.S. age-adjusted drug overdose death rate was 32.4 per 100,000 population.The highest rates were in West Virginia (90.9) and the District of Columbia (63.6); the lowest rates were in the Upper Midwest and Texas.The lowest state rates were those in Nebraska (11.4),South Dakota (12.6), and Iowa (15.3).